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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 4-1983899-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=1983899&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 7,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "NELFA",
"hgnc_id": 12768,
"hgvs_c": "c.1251G>A",
"hgvs_p": "p.Pro417Pro",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -7,
"transcript": "NM_005663.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7",
"acmg_score": -7,
"allele_count_reference_population": 43,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.66,
"chr": "4",
"clinvar_classification": "Likely benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.6600000262260437,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 528,
"aa_ref": "P",
"aa_start": 417,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2198,
"cdna_start": 1266,
"cds_end": null,
"cds_length": 1587,
"cds_start": 1251,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_005663.5",
"gene_hgnc_id": 12768,
"gene_symbol": "NELFA",
"hgvs_c": "c.1251G>A",
"hgvs_p": "p.Pro417Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000382882.9",
"protein_coding": true,
"protein_id": "NP_005654.4",
"strand": false,
"transcript": "NM_005663.5",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 528,
"aa_ref": "P",
"aa_start": 417,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2198,
"cdna_start": 1266,
"cds_end": null,
"cds_length": 1587,
"cds_start": 1251,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000382882.9",
"gene_hgnc_id": 12768,
"gene_symbol": "NELFA",
"hgvs_c": "c.1251G>A",
"hgvs_p": "p.Pro417Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005663.5",
"protein_coding": true,
"protein_id": "ENSP00000372335.4",
"strand": false,
"transcript": "ENST00000382882.9",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 539,
"aa_ref": "P",
"aa_start": 428,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2465,
"cdna_start": 1527,
"cds_end": null,
"cds_length": 1620,
"cds_start": 1284,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000542778.5",
"gene_hgnc_id": 12768,
"gene_symbol": "NELFA",
"hgvs_c": "c.1284G>A",
"hgvs_p": "p.Pro428Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000445757.2",
"strand": false,
"transcript": "ENST00000542778.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1707,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000467661.5",
"gene_hgnc_id": 12768,
"gene_symbol": "NELFA",
"hgvs_c": "n.775G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000467661.5",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 568,
"aa_ref": "P",
"aa_start": 457,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2318,
"cdna_start": 1386,
"cds_end": null,
"cds_length": 1707,
"cds_start": 1371,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000898322.1",
"gene_hgnc_id": 12768,
"gene_symbol": "NELFA",
"hgvs_c": "c.1371G>A",
"hgvs_p": "p.Pro457Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000568381.1",
"strand": false,
"transcript": "ENST00000898322.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 556,
"aa_ref": "P",
"aa_start": 445,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2282,
"cdna_start": 1350,
"cds_end": null,
"cds_length": 1671,
"cds_start": 1335,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000898321.1",
"gene_hgnc_id": 12768,
"gene_symbol": "NELFA",
"hgvs_c": "c.1335G>A",
"hgvs_p": "p.Pro445Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000568380.1",
"strand": false,
"transcript": "ENST00000898321.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 532,
"aa_ref": "P",
"aa_start": 421,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2188,
"cdna_start": 1263,
"cds_end": null,
"cds_length": 1599,
"cds_start": 1263,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000416258.5",
"gene_hgnc_id": 12768,
"gene_symbol": "NELFA",
"hgvs_c": "c.1263G>A",
"hgvs_p": "p.Pro421Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000387647.1",
"strand": false,
"transcript": "ENST00000416258.5",
"transcript_support_level": 5
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 530,
"aa_ref": "P",
"aa_start": 419,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2204,
"cdna_start": 1272,
"cds_end": null,
"cds_length": 1593,
"cds_start": 1257,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000911416.1",
"gene_hgnc_id": 12768,
"gene_symbol": "NELFA",
"hgvs_c": "c.1257G>A",
"hgvs_p": "p.Pro419Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581475.1",
"strand": false,
"transcript": "ENST00000911416.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 526,
"aa_ref": "P",
"aa_start": 415,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2209,
"cdna_start": 1273,
"cds_end": null,
"cds_length": 1581,
"cds_start": 1245,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000898320.1",
"gene_hgnc_id": 12768,
"gene_symbol": "NELFA",
"hgvs_c": "c.1245G>A",
"hgvs_p": "p.Pro415Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000568379.1",
"strand": false,
"transcript": "ENST00000898320.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 518,
"aa_ref": "P",
"aa_start": 407,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2165,
"cdna_start": 1236,
"cds_end": null,
"cds_length": 1557,
"cds_start": 1221,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000967102.1",
"gene_hgnc_id": 12768,
"gene_symbol": "NELFA",
"hgvs_c": "c.1221G>A",
"hgvs_p": "p.Pro407Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000637161.1",
"strand": false,
"transcript": "ENST00000967102.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 502,
"aa_ref": "P",
"aa_start": 391,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2118,
"cdna_start": 1186,
"cds_end": null,
"cds_length": 1509,
"cds_start": 1173,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000967101.1",
"gene_hgnc_id": 12768,
"gene_symbol": "NELFA",
"hgvs_c": "c.1173G>A",
"hgvs_p": "p.Pro391Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000637160.1",
"strand": false,
"transcript": "ENST00000967101.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 474,
"aa_ref": "P",
"aa_start": 363,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2026,
"cdna_start": 1102,
"cds_end": null,
"cds_length": 1425,
"cds_start": 1089,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000967103.1",
"gene_hgnc_id": 12768,
"gene_symbol": "NELFA",
"hgvs_c": "c.1089G>A",
"hgvs_p": "p.Pro363Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000637162.1",
"strand": false,
"transcript": "ENST00000967103.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 556,
"aa_ref": "P",
"aa_start": 445,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2282,
"cdna_start": 1350,
"cds_end": null,
"cds_length": 1671,
"cds_start": 1335,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_017008589.3",
"gene_hgnc_id": 12768,
"gene_symbol": "NELFA",
"hgvs_c": "c.1335G>A",
"hgvs_p": "p.Pro445Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864078.2",
"strand": false,
"transcript": "XM_017008589.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2228,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000333877.8",
"gene_hgnc_id": 12768,
"gene_symbol": "NELFA",
"hgvs_c": "n.*818G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000330311.4",
"strand": false,
"transcript": "ENST00000333877.8",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2495,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000463820.5",
"gene_hgnc_id": 12768,
"gene_symbol": "NELFA",
"hgvs_c": "n.1570G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000463820.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2228,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000333877.8",
"gene_hgnc_id": 12768,
"gene_symbol": "NELFA",
"hgvs_c": "n.*818G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000330311.4",
"strand": false,
"transcript": "ENST00000333877.8",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs376124758",
"effect": "synonymous_variant",
"frequency_reference_population": 0.000026876647,
"gene_hgnc_id": 12768,
"gene_symbol": "NELFA",
"gnomad_exomes_ac": 24,
"gnomad_exomes_af": 0.0000165777,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 19,
"gnomad_genomes_af": 0.000124859,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -4.209,
"pos": 1983899,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_005663.5"
}
]
}